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+\name{mergeGostatsResults}

+\alias{mergeGostatsResults}

+\title{Merge enrichment results obtained for different databases into one file per component.}

+\usage{

+  mergeGostatsResults(resPath, GOstatsPath,

+    rdata = "hgres", cutoffs = NULL, hgCutoff = 0.01,

+    cond = TRUE, pathGenes)

+}

+\arguments{

+  \item{resPath}{The global path where results of ICA

+  analysis are written}

+

+  \item{GOstatsPath}{The path within argument

+  \code{resPath} where files will be written}

+

+  \item{rdata}{The name of the rdata file containing the

+  enrichment analysis of all components}

+

+  \item{cutoffs}{The threshold(s) used to select genes used

+  in enrichment analysis}

+

+  \item{hgCutoff}{The p-value threshold}

+

+  \item{cond}{A logical indicating whether the calculation

+  has been conditioned on the GO structure, see

+  \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}

+

+  \item{pathGenes}{The path where HTML files containing

+  gene projections for each component are located}

+}

+\value{

+  NULL

+}

+\description{

+  This function is internal and called by function

+  \code{runEnrich}. It merges enrichment results obtained

+  with either KEGG, GO, or both databases into one file.

+}

+\details{

+  This function writes an HTML file per component,

+  containing the outputs of the enrichment tests computed

+  through the function \code{\link[Category]{hyperGTest}}.

+  The results of the enrichment tests are loaded from .rda

+  files located in

+  \code{resPath(icaSet)}/GOstatsEnrichAnalysis/byDb/'db-name'/('ontology-name'/).

+  The results obtained for the different

+  databases/ontologies are then merged into an array for

+  each component, this array is written as an HTML file in

+  the directory

+  \code{resPath(icaSet)}/\code{zvalCutoff(params)}. The

+  arguments \code{hgCutoff} and \code{cond} have to be

+  provided because they will be used in the file names of

+  the resulting files.

+

+  This function makes several important assumptions: only

+  databases GO and KEGG have been tested, p-values are not

+  available for gene sets that have not been selected as

+  significant.

+

+  The outputs of \code{\link[Category]{hyperGTest}} that

+  are given in each table are: \describe{ \item{DB, ID,

+  Term}{The database, the gene set ID, and the gene set

+  name,} \item{P-value}{probability of observing the number

+  of genes annotated for the gene set among the selected

+  gene list, knowing the total number of annotated genes

+  among the universe}, \item{Expected counts}{expected

+  number of genes in the selected gene list to be found at

+  each tested category term/gene set,} \item{Odds

+  ratio}{odds ratio for each category term tested which is

+  an indicator of the level of enrichment of genes within

+  the list as against the universe,} \item{Counts}{number

+  of genes in the selected gene list which are annotated

+  for the gene set,} \item{Size}{number of genes from the

+  universe annotated for the gene set.}}

+}

+\author{

+  Anne Biton

+}

+\seealso{

+  \code{\link[xtable]{xtable}},

+  \code{\link[biomaRt]{useMart}},

+  \code{\link[Category]{hyperGTest}},

+  \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}},

+  \code{\link{hypergeoAn}},

+  \code{\link{mergeGostatsResults}}

+}

+\keyword{internal}

+